FMO DATABASE

FMODB ID: VY5Q1

Calculation Name: 1TWF-F-Xray547

Preferred Name:

Target Type:

Ligand Name: uridine 5'-triphosphate | manganese (ii) ion | zinc ion

Ligand 3-letter code: UTP | MN | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TWF

Chain ID: F

ChEMBL ID:

UniProt ID: P20434

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	84
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-556279.224139
FMO2-HF: Nuclear repulsion	522471.36178
FMO2-HF: Total energy	-33807.862358
FMO2-MP2: Total energy	-33906.413022

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:72:LYS)

Summations of interaction energy for fragment #1(A:72:LYS)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-208.484	-213.47	32.268	-13.119	-14.165	-0.173

Interaction energy analysis for fragmet #1(A:72:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.655 / q_NPA : 1.827

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	74	ILE	0	0.027	0.026	3.897	-7.274	-5.808	-0.010	-0.761	-0.696	-0.002
64	A	135	ARG	1	0.813	0.873	4.698	65.839	65.886	-0.001	-0.004	-0.042	0.000
66	A	137	TYR	0	-0.017	-0.022	4.457	-8.011	-7.911	-0.001	-0.012	-0.086	0.000
69	A	140	ASP	-1	-0.812	-0.867	4.751	-95.260	-95.139	-0.001	-0.008	-0.112	0.000
70	A	141	GLY	0	-0.022	-0.004	3.812	-14.125	-13.444	0.006	-0.292	-0.395	-0.001
71	A	142	SER	0	-0.117	-0.095	1.677	-51.050	-53.139	16.412	-8.636	-5.688	-0.072
72	A	143	PHE	0	0.111	0.017	2.072	-15.454	-20.790	15.864	-3.383	-7.145	-0.098
73	A	144	GLU	-1	-0.722	-0.824	3.961	-50.602	-50.578	-0.001	-0.023	-0.001	0.000
4	A	75	PRO	0	-0.012	0.003	6.625	2.334	2.334	0.000	0.000	0.000	0.000
5	A	76	LYS	1	0.958	0.973	10.323	33.648	33.648	0.000	0.000	0.000	0.000
6	A	77	ASP	-1	-0.857	-0.921	12.957	-32.606	-32.606	0.000	0.000	0.000	0.000
7	A	78	GLN	0	-0.052	-0.054	11.344	-5.868	-5.868	0.000	0.000	0.000	0.000
8	A	79	ARG	1	0.745	0.874	10.194	40.041	40.041	0.000	0.000	0.000	0.000
9	A	80	ALA	0	0.011	0.005	11.507	3.087	3.087	0.000	0.000	0.000	0.000
10	A	81	THR	0	-0.085	-0.047	10.762	1.650	1.650	0.000	0.000	0.000	0.000
11	A	82	THR	0	0.010	0.000	13.368	0.810	0.810	0.000	0.000	0.000	0.000
12	A	83	PRO	0	0.028	0.016	16.262	-0.827	-0.827	0.000	0.000	0.000	0.000
13	A	84	TYR	0	0.022	0.030	18.260	0.195	0.195	0.000	0.000	0.000	0.000
14	A	85	MET	0	-0.029	0.016	18.115	-1.529	-1.529	0.000	0.000	0.000	0.000
15	A	86	THR	0	0.022	-0.013	17.364	1.345	1.345	0.000	0.000	0.000	0.000
16	A	87	LYS	1	1.007	0.986	19.903	23.671	23.671	0.000	0.000	0.000	0.000
17	A	88	TYR	0	0.019	0.000	18.835	0.663	0.663	0.000	0.000	0.000	0.000
18	A	89	GLU	-1	-0.758	-0.827	14.630	-35.800	-35.800	0.000	0.000	0.000	0.000
19	A	90	ARG	1	1.031	1.020	18.401	22.001	22.001	0.000	0.000	0.000	0.000
20	A	91	ALA	0	-0.011	-0.003	21.905	0.576	0.576	0.000	0.000	0.000	0.000
21	A	92	ARG	1	0.973	0.983	14.148	34.672	34.672	0.000	0.000	0.000	0.000
22	A	93	ILE	0	0.013	0.020	17.936	0.105	0.105	0.000	0.000	0.000	0.000
23	A	94	LEU	0	0.005	0.006	20.677	0.616	0.616	0.000	0.000	0.000	0.000
24	A	95	GLY	0	0.025	0.017	23.797	0.745	0.745	0.000	0.000	0.000	0.000
25	A	96	THR	0	-0.072	-0.057	19.465	0.168	0.168	0.000	0.000	0.000	0.000
26	A	97	ARG	1	0.727	0.807	22.500	22.284	22.284	0.000	0.000	0.000	0.000
27	A	98	ALA	0	0.037	0.020	24.486	0.665	0.665	0.000	0.000	0.000	0.000
28	A	99	LEU	0	0.013	0.011	23.989	0.542	0.542	0.000	0.000	0.000	0.000
29	A	100	GLN	0	0.014	0.011	21.441	0.997	0.997	0.000	0.000	0.000	0.000
30	A	101	ILE	0	0.014	0.015	26.678	0.552	0.552	0.000	0.000	0.000	0.000
31	A	102	SER	0	-0.076	-0.045	29.726	0.652	0.652	0.000	0.000	0.000	0.000
32	A	103	MET	0	-0.061	-0.027	25.926	0.385	0.385	0.000	0.000	0.000	0.000
33	A	104	ASN	0	-0.036	-0.019	31.113	0.469	0.469	0.000	0.000	0.000	0.000
34	A	105	ALA	0	-0.018	0.008	27.639	0.075	0.075	0.000	0.000	0.000	0.000
35	A	106	PRO	0	0.003	-0.008	28.620	0.255	0.255	0.000	0.000	0.000	0.000
36	A	107	VAL	0	0.020	0.026	28.874	-0.727	-0.727	0.000	0.000	0.000	0.000
37	A	108	PHE	0	-0.046	-0.023	25.039	0.199	0.199	0.000	0.000	0.000	0.000
38	A	109	VAL	0	-0.053	-0.027	29.797	-0.035	-0.035	0.000	0.000	0.000	0.000
39	A	110	ASP	-1	-0.862	-0.924	32.445	-15.299	-15.299	0.000	0.000	0.000	0.000
40	A	111	LEU	0	0.005	0.007	34.862	-0.144	-0.144	0.000	0.000	0.000	0.000
41	A	112	GLU	-1	-0.853	-0.912	37.623	-14.982	-14.982	0.000	0.000	0.000	0.000
42	A	113	GLY	0	-0.044	-0.021	40.221	0.040	0.040	0.000	0.000	0.000	0.000
43	A	114	GLU	-1	-0.866	-0.926	36.361	-15.955	-15.955	0.000	0.000	0.000	0.000
44	A	115	THR	0	0.000	-0.010	37.829	-0.183	-0.183	0.000	0.000	0.000	0.000
45	A	116	ASP	-1	-0.825	-0.902	33.816	-17.771	-17.771	0.000	0.000	0.000	0.000
46	A	117	PRO	0	0.041	0.020	30.671	-0.262	-0.262	0.000	0.000	0.000	0.000
47	A	118	LEU	0	0.006	-0.009	28.185	-0.706	-0.706	0.000	0.000	0.000	0.000
48	A	119	ARG	1	0.797	0.877	30.304	16.068	16.068	0.000	0.000	0.000	0.000
49	A	120	ILE	0	0.026	0.020	30.939	-0.114	-0.114	0.000	0.000	0.000	0.000
50	A	121	ALA	0	0.011	0.011	26.563	-0.312	-0.312	0.000	0.000	0.000	0.000
51	A	122	MET	0	-0.062	-0.051	27.425	-0.693	-0.693	0.000	0.000	0.000	0.000
52	A	123	LYS	1	0.823	0.917	29.237	16.363	16.363	0.000	0.000	0.000	0.000
53	A	124	GLU	-1	-0.713	-0.832	26.824	-21.215	-21.215	0.000	0.000	0.000	0.000
54	A	125	LEU	0	-0.045	-0.033	22.873	-0.663	-0.663	0.000	0.000	0.000	0.000
55	A	126	ALA	0	-0.032	-0.010	26.065	-0.427	-0.427	0.000	0.000	0.000	0.000
56	A	127	GLU	-1	-0.825	-0.925	28.992	-18.001	-18.001	0.000	0.000	0.000	0.000
57	A	128	LYS	1	0.734	0.867	22.030	24.950	24.950	0.000	0.000	0.000	0.000
58	A	129	LYS	1	0.901	0.948	25.348	18.479	18.479	0.000	0.000	0.000	0.000
59	A	130	ILE	0	0.000	-0.003	20.800	0.081	0.081	0.000	0.000	0.000	0.000
60	A	131	PRO	0	0.031	0.035	20.609	-1.084	-1.084	0.000	0.000	0.000	0.000
61	A	132	LEU	0	-0.041	-0.027	17.010	-0.905	-0.905	0.000	0.000	0.000	0.000
62	A	133	VAL	0	0.004	-0.011	11.218	0.126	0.126	0.000	0.000	0.000	0.000
63	A	134	ILE	0	-0.029	-0.004	11.619	-0.545	-0.545	0.000	0.000	0.000	0.000
65	A	136	ARG	1	0.790	0.855	8.528	38.964	38.964	0.000	0.000	0.000	0.000
67	A	138	LEU	0	0.031	0.030	5.545	8.932	8.932	0.000	0.000	0.000	0.000
68	A	139	PRO	0	0.008	-0.011	6.843	-6.513	-6.513	0.000	0.000	0.000	0.000
74	A	145	ASP	-1	-0.789	-0.851	7.262	-61.112	-61.112	0.000	0.000	0.000	0.000
75	A	146	TRP	0	-0.014	-0.020	9.235	3.720	3.720	0.000	0.000	0.000	0.000
76	A	147	SER	0	-0.005	-0.005	12.943	0.789	0.789	0.000	0.000	0.000	0.000
77	A	148	VAL	0	0.014	-0.007	15.831	0.609	0.609	0.000	0.000	0.000	0.000
78	A	149	GLU	-1	-0.921	-0.951	18.687	-25.414	-25.414	0.000	0.000	0.000	0.000
79	A	150	GLU	-1	-0.823	-0.892	15.772	-34.602	-34.602	0.000	0.000	0.000	0.000
80	A	151	LEU	0	-0.032	0.000	15.480	0.350	0.350	0.000	0.000	0.000	0.000
81	A	152	ILE	0	0.017	0.007	19.307	1.249	1.249	0.000	0.000	0.000	0.000
82	A	153	VAL	0	-0.039	-0.036	22.202	-0.745	-0.745	0.000	0.000	0.000	0.000
83	A	154	ASP	-1	-0.929	-0.965	24.394	-19.874	-19.874	0.000	0.000	0.000	0.000
84	A	155	LEU	-1	-0.999	-0.985	22.720	-21.756	-21.756	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:72:LYS)